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Results: 1 to 20 of 86

1.

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.

Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J.

Genome Biol. 2012 Aug 3;13(8):R67. doi: 10.1186/gb-2012-13-8-r67.

PMID:
22863408
[PubMed - in process]
Free PMC Article
2.

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

J Vis Exp. 2011 Apr 30;(50). pii: 2638. doi: 10.3791/2638.

PMID:
21559008
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

iCLIP: protein-RNA interactions at nucleotide resolution.

Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J.

Methods. 2014 Feb;65(3):274-87. doi: 10.1016/j.ymeth.2013.10.011. Epub 2013 Oct 25.

PMID:
24184352
[PubMed - in process]
Free PMC Article
4.

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.

Zhang C, Darnell RB.

Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.

PMID:
21633356
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

Nat Struct Mol Biol. 2010 Jul;17(7):909-15. doi: 10.1038/nsmb.1838. Epub 2010 Jul 4.

PMID:
20601959
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.

PMID:
20644507
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.

Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M.

Nat Methods. 2011 May 15;8(7):559-64. doi: 10.1038/nmeth.1608.

PMID:
21572407
[PubMed - indexed for MEDLINE]
8.

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB.

Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9.

PMID:
24407355
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.

Yun J, Wang T, Xiao G.

Biometrics. 2014 Jun;70(2):430-40. doi: 10.1111/biom.12147. Epub 2014 Feb 24.

PMID:
24571656
[PubMed - in process]
Free PMC Article
10.

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.

Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A.

RNA Biol. 2014 Feb;11(2):146-55. doi: 10.4161/rna.27991. Epub 2014 Feb 7.

PMID:
24526010
[PubMed - in process]
Free PMC Article
11.

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data.

Li JH, Liu S, Zhou H, Qu LH, Yang JH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D92-7. doi: 10.1093/nar/gkt1248. Epub 2013 Dec 1.

PMID:
24297251
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1.

Wang X, Juan L, Lv J, Wang K, Sanford JR, Liu Y.

BMC Genomics. 2011 Dec 23;12 Suppl 5:S8. doi: 10.1186/1471-2164-12-S5-S8. Epub 2011 Dec 23.

PMID:
22369183
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.

Chen B, Yun J, Kim MS, Mendell JT, Xie Y.

Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.

PMID:
24451213
[PubMed - in process]
Free PMC Article
14.

CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.

Wang Z, Tollervey J, Briese M, Turner D, Ule J.

Methods. 2009 Jul;48(3):287-93. doi: 10.1016/j.ymeth.2009.02.021. Epub 2009 Mar 9.

PMID:
19272451
[PubMed - indexed for MEDLINE]
15.

CLIP identifies Nova-regulated RNA networks in the brain.

Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB.

Science. 2003 Nov 14;302(5648):1212-5.

PMID:
14615540
[PubMed - indexed for MEDLINE]
Free Article
16.

A model-based approach to identify binding sites in CLIP-Seq data.

Wang T, Chen B, Kim M, Xie Y, Xiao G.

PLoS One. 2014 Apr 8;9(4):e93248. doi: 10.1371/journal.pone.0093248. eCollection 2014.

PMID:
24714572
[PubMed - in process]
Free PMC Article
17.

Prediction of clustered RNA-binding protein motif sites in the mammalian genome.

Zhang C, Lee KY, Swanson MS, Darnell RB.

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.

PMID:
23685613
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

CLIP: a method for identifying protein-RNA interaction sites in living cells.

Ule J, Jensen K, Mele A, Darnell RB.

Methods. 2005 Dec;37(4):376-86.

PMID:
16314267
[PubMed - indexed for MEDLINE]
19.

Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq.

Yao C, Weng L, Shi Y.

Methods Mol Biol. 2014;1126:399-410. doi: 10.1007/978-1-62703-980-2_27.

PMID:
24549678
[PubMed - in process]
20.

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.

Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, Weng SL, Shrestha S, Hsiao CC, Hung JH, Huang HD.

BMC Genomics. 2013;14 Suppl 1:S2. doi: 10.1186/1471-2164-14-S1-S2. Epub 2013 Jan 21.

PMID:
23368412
[PubMed - indexed for MEDLINE]
Free PMC Article

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